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UniProtKB/Swiss-Prot O60341: Variant p.Asp556Gly

Lysine-specific histone demethylase 1A
Gene: KDM1A
Variant information

Variant position:  556
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  LP/P [Disclaimer]
The variants are classified into three categories: LP/P, LB/B and US.
  • LP/P: likely pathogenic or pathogenic.
  • LB/B: likely benign or benign.
  • US: uncertain significance

Residue change:  From Aspartate (D) to Glycine (G) at position 556 (D556G, p.Asp556Gly).
Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.

Physico-chemical properties:  Change from medium size and acidic (D) to glycine (G)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -1
The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:
  • Lowest score: -4 (low probability of substitution).
  • Highest score: 11 (high probability of substitution).
More information can be found on the following page

Variant description:  In CPRF.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  556
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  852
The length of the canonical sequence.

Location on the sequence:   LEFANATPLSTLSLKHWDQD  D DFEFTGSHLTVRNGYSCVPV
The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.

Residue conservation: 
The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         LEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPV

Mouse                         LEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPV

Sequence annotation in neighborhood:  
The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:
  • Type: the type of sequence feature.
  • Positions: endpoints of the sequence feature.
  • Description: contains additional information about the feature.

TypePositionsDescription
Chain 1 – 852 Lysine-specific histone demethylase 1A
Region 300 – 852 Demethylase activity
Mutagenesis 564 – 564 H -> A. Strongly reduces demethylase activity.
Helix 556 – 558


Literature citations

Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study.
Rauch A.; Wieczorek D.; Graf E.; Wieland T.; Endele S.; Schwarzmayr T.; Albrecht B.; Bartholdi D.; Beygo J.; Di Donato N.; Dufke A.; Cremer K.; Hempel M.; Horn D.; Hoyer J.; Joset P.; Roepke A.; Moog U.; Riess A.; Thiel C.T.; Tzschach A.; Wiesener A.; Wohlleber E.; Zweier C.; Ekici A.B.; Zink A.M.; Rump A.; Meisinger C.; Grallert H.; Sticht H.; Schenck A.; Engels H.; Rappold G.; Schroeck E.; Wieacker P.; Riess O.; Meitinger T.; Reis A.; Strom T.M.;
Lancet 380:1674-1682(2012)
Cited for: VARIANT CPRF GLY-556;

Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features.
Chong J.X.; Yu J.H.; Lorentzen P.; Park K.M.; Jamal S.M.; Tabor H.K.; Rauch A.; Saenz M.S.; Boltshauser E.; Patterson K.E.; Nickerson D.A.; Bamshad M.J.;
Genet. Med. 18:788-795(2016)
Cited for: VARIANTS CPRF LYS-379; GLY-556 AND HIS-761;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.